Using Geneticsland R API

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Contents

Introduction

The Land R API functions are provided to users who want to query Geneticsland data content and perform separate analyses or build custom charts. In this example, we will generate a forest plot from GWAS in GxL.Associations_B37.

Note that if this is the first time you have used the Land R API please visit Land R API for instructions on how to install Oshell.

Load R API from Omicsoft website

Load R API from Omicsoft website

load(url("http://omicsoft.com/downloads/land/Rapi/Land_R_API.Rda"))
Land.Help() 
####################################################################################################
#################################### Omicsoft Land R API ###########################################
                        Welcome to use Land R API of Omicsoft!
To begin with, you should initiate Oshell environment and Land environment.

Initiate Oshell environment:
Land.InitiateOshell(
        MonoPath = MonoPath,
 OshellDirectory = OshellDirectory,
   BaseDirectory = BaseDirectory,
   TempDirectory = TempDirectory
   );
eg.
#For Windows:
Land.InitiateOshell(
    OshellDirectory = "E:/Oshell/",
     BaseDirectory  = "C:/Users/Leon/Documents/Omicsoft",
      TempDirectory = "C:/Users/Leon/Documents/Omicsoft/Temp"
     );

Initiate Land environment

#Initiate Land environment
Land.InitiateLand(Server = "192.168.1.106:8065", UserID = "userName", Password = "password", LandName = "GxL.Associations_B37")

Perform Search, Select View, and Generate plots

GeneticsLand

Search for gene, phenotype, association report, region, or RS_ID

#Initializes Search
search <- "egfr"
#Sets view
view <- "Gene.CodingSnpListing"
#Performs the search
result <-Land.SearchGeneticLand(Search=search, View=view)


The screen shots below provide real use cases. In this example a very basic Forestplot was created using ggplot2.

RAPIsearchresults.png

ForestPlot.png